← Back to search
1dde

STRUCTURE OF THE DNAG CATALYTIC CORE

Method: X-RAY DIFFRACTION Dmax: 78.1 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA PRIMASE

Escherichia coli

UniProt P0ABS5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 111–433 Fragment：36 KDA CATALYTIC CORE DOMAIN Y1 YTTRIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM YCL2, VAPOR DIFFUSION, HANGING DROP Resolution 1.70 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1DDE Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DD9 STRUCTURE OF THE DNAG CATALYTIC CORE Deposited 1999-11-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 111–433（323 aa） Fragment：36 KDA CATALYTIC CORE DOMAIN
Not recorded SR STRONTIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；18-21% PEG4000, 5% PEG200, 30% ETHYLENE GLYCOL, 0.2M AMMONIUM ACETATE, 0.05M SODIUM ACETATE, PH 5.0, 0.1% DIOXANE, 2-8 MM SRCL2, VAPOR DIFFUSION, HANGING DROP
Resolution 1.60 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1EQN E.COLI PRIMASE CATALYTIC CORE Deposited 2000-04-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 109–429（321 aa） Fragment：CATALYTIC CORE
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；PEG 4000, DTT, Tris/HCl, sodium acetate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.276
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 434–581（148 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
1T3W Crystal Structure of the E.coli DnaG C-terminal domain (residues 434 to 581) Deposited 2004-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 434–581（148 aa）
Chain B 434–581（148 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% v/v PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
2HAJ Solution structure of the helicase-binding domain of Escherichia coli primase Deposited 2006-06-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：Helicase-binding domain, residues 447-581
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure 1
NMR sample composition 0.3mM DnaG-C U-15N, 13C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3mM DnaG-C; 10mM phosphate buffer(pH 6.10); 100mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3B39 Structure of the DnaG primase catalytic domain bound to ssDNA Deposited 2007-10-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 111–429（319 aa） Fragment：RNA Polymerase Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.35 Å R-free 0.254
3B39 Structure of the DnaG primase catalytic domain bound to ssDNA Deposited 2007-10-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 111–429（319 aa） Fragment：RNA Polymerase Domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；21% PEG 4000, 100 mM ammonium acetate, 50 mM sodium acetate (pH 5.0), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.35 Å R-free 0.254
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6
Resolution 1.50 Å R-free 0.179
6CBR DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 131-139)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；10% w/v PEG3000, 5 mM zinc acetate, 5 mM 1,10-phenanthroline, 100 mM sodium acetate, pH 4.6
Resolution 1.50 Å R-free 0.179
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 3 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 1.85 Å R-free 0.224
6CBS DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 3 ACY ACETIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；7.5% w/v PEG3000, 15 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 1.85 Å R-free 0.224
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 2 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 2.10 Å R-free 0.229
6CBT DnaG Primase C-terminal domain complex with SSB C-terminal peptide Deposited 2018-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 434–581（148 aa） Fragment：DnaG C-terminal domain (UNP residues 434-581), linker peptide, SSB C-terminal peptide (UNP residues 130-139)
Not recorded ZN ZINC ION × 1 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；9.5% w/v PEG3000, 10 mM zinc acetate, 100 mM sodium acetate, pH 4.6
Resolution 2.10 Å R-free 0.229
7T22 E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2021-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: decameric
Chain G 434–581（148 aa） Fragment：C-terminal domain
Chain H 434–581（148 aa） Fragment：C-terminal domain
Chain I 434–581（148 aa） Fragment：C-terminal domain
Mutation：R568C Mutation：R568C Mutation：R568C ADP ADENOSINE-5'-DIPHOSPHATE × 5 ALF TETRAFLUOROALUMINATE ION × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP.
cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.
Resolution 4.20 Å
9ECO E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 Deposited 2024-11-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: nonameric
Chain G 434–581（148 aa） Fragment：C-terminal domain
Chain H 434–581（148 aa） Fragment：C-terminal domain
Mutation：R568C Mutation：R568C ALF TETRAFLUOROALUMINATE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM Tris-HCl, pH 7.6, 100 mM NaCl, 5 mM MgCl2, 3 mM DTT, 0.25 mM EDTA and 100 micromolar ADP, 0.5 mM AlCl3, 5 mM NaF.
cryo-EM vitrification conditions Cryogen ETHANE；3 microL of sample was applied to glow-discharged grids. Grids were blotted at 6 degrees C for 3.5 s with no extra blot force.
Resolution 2.83 Å

10 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRIM_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 16–338； UniProt 111–433

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1dde

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dde
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1dde
Deposition date deposition_date1999-11-09
Structure title titleSTRUCTURE OF THE DNAG CATALYTIC CORE
Keywords keywordsTOPRIM, 3-HELIX BUNDLE, DNA-BINDING PROTEIN, RNA POLYMERASE, REPLICATION PROTEIN, PRIMASE, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.19 Å
Radius of gyration Rg (electron density) rg_electron22.53 Å
Forward intensity I(0) i022309300.00
Molecular weight molecular_weight35231.0 kDa
Excluded volume excluded_volume43691 ų
Envelope volume envelope_volume51749 ų
Hydration-shell volume shell_volume20387 ų
Envelope diameter envelope_diameter82.6 Å
Shell Rg shell_rg28.19 Å
Envelope Rg envelope_rg22.94 Å
Shape Rg shape_rg22.55 Å
Total Rg total_rg23.17 Å
Total atoms total_atoms2460
Residues n_residues310
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.1 Å
Rg (real space) rg_real23.33 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real2.2310e+07
I(0) uncertainty (real space) i0_real_error3.3820e+05
Rg (reciprocal space) rg_reciprocal23.30 Å
I(0) (reciprocal space) i0_reciprocal22310000.0000
Solution quality estimate total_estimate0.7870
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.0 Å
Skewness Skewness skewness0.550
Kurtosis Kurtosis kurtosis-0.094
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4835000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1ddea_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.13 — DNA primase core
Superfamily Superfamily superfamilye.13.1 — DNA primase core
Family Family familye.13.1.1 — DNA primase DnaG catalytic core

CATH v4.4 (3 domains)

Domain ID domain_id1ddeA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily10 — DNA primase, catalytic core, N-terminal domain
Domain ID domain_id1ddeA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1ddeA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology50 — Pheromone ER-1
Homologous superfamily homologous superfamily20 — DnaG, RNA polymerase domain, helical bundle
▶

8. Citations (1)

▶

9. Files and Curves (10)